The Conservative chairwoman, Lady Warsi, has stepped out of line with David Cameron, condemning some of the constituency boundary changes proposed by the Boundary Commission as "mad and insane".

Warsi's remarks came in a briefing for regional reporters. The prime minister has been touring regional meetings at the Conservative party conference, saying the plans are logical and the number of Tory-held seats likely to be lost due to changes will be minimal and politically manageable.

Warsi said the party would appeal against some of the Boundary Commission's proposals, which will cut the number of MPs at Westminster from 650 to 600 and ensure constituencies contain similar numbers of voters.

She insisted the overall plan was correct, even though not everyone in the party would be "entirely content" with the changes.

"The proposals have come out from the Boundary Commission," she said.

"The Boundary Commission is an independent organisation, and I agree with some of our MPs that some of the proposals are mad and insane.

"I know Yorkshire very well, and there are parts of Yorkshire that have been carved out in a very unusual way. So I think there is scope for us as a party and, of course, as individual MPs, to make representations to the Boundary Commission about how [we] feel the more natural boundary for that association lies.

"There's an appeals process, and we will be submitting appeals as part and parcel of that."

All three main parties have promised to cut the cost of politics, and Warsi said: "We can't say: 'We thought it was a great idea, but now it's happening in reality it's not going to be me'.

"This is the same argument about 'yes, we believe that cuts should be made but not in my department' – 'yes, we believe that the cost of politics should be reduced and boundaries should be reduced, but not my boundaries'.

"So we have to take an overall view of what we are trying to achieve."

She said the current level of variation in the number of constituents within each seat "can't be right".

Critics claim the controversial proposals are the direct result of the government insisting in the legislation that the commission only allows a 5 % variation either way from a target number of constituents in each seat.

As a result, the commission has been forced to ignore county borders and city councils, leaving constituencies with structures that ignore physical, natural and administrative boundaries.

It has been given little leeway in the appeals and in some counties, such as Cumbria, political parties are clubbing together to come up with more rational proposals.

"It's staggering that it's taken her this long to realise the damaging impact of this Tory legislation. Labour has consistently said that the boundary changes will lead to the break-up of communities, but the Tory-led government refuse to acknowledge the impact of their actions."